Sequence
atgc intronic sequence ATGC exonic sequencegtagcctgtggtgtttctaagttgttcttcccaaggatttggagctcactctctttcttggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAG
Basic information
species | Selaginella moellendorffii |
transcript | EFJ36458 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ36458 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os10g28200.1 (Oryza sativa), 3'ss of exon 2
---------------------------------------gtagcctgtggtgtttctaagttgttcttcccaaggatttggagctcactctctttcttggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAG
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gtccggctctctcttttttttttacatatttttactgttatatctcagcttagcctgagcttgttttatccatatcaattcatttgttacaactaatggtcctacagGTTCTTCTATGCCTCAAGTGCATGCATTTACCCTGAATTCAAGCAGCTTGAAACTAACGTTAGCCTGAAGGAATCTGATGCCTGGCCTGCTGAG
upper sequence: EFJ36458 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os11g37890.2 (Oryza sativa), 3'ss of exon 2
--------------------------------gtagcctgtggtgtttctaagttgttcttcccaaggatttggagctcactctctttcttggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAG
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aaccctagaattcctcaaaacagagcatttactttaacaatcctgtcatgttatcatcactcagaagaatcatcattttggttattttttttccttgtagGTTCTTTTATGCTTCAAGTGCTTGTATCTACCCTGAATTTAAGCAGCTGGACACTGTAGTTAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAG
upper sequence: EFJ36458 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os11g37890.3 (Oryza sativa), 3'ss of exon 2
--------------------------------gtagcctgtggtgtttctaagttgttcttcccaaggatttggagctcactctctttcttggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAG------
| | | ||| | | || ||| || | | | ||| || ||| || || |||||||| || ||||| || || ||||| || |||||||||||||| ||| || || ||||||||||||||||| ||||| ||||||
aaccctagaattcctcaaaacagagcatttactttaacaatcctgtcatgttatcatcactcagaagaatcatcattttggttattttttttccttgtagGTTCTTTTATGCTTCAAGTGCTTGTATCTACCCTGAATTTAAGCAGCTGGACACTGTAGTTAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAGGTTTCT
upper sequence: EFJ36458 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G124434_T01 (Zea mays), 3'ss of exon 2
-----------------------------------------------------------gtagcctg--tggtgtttctaagttgttcttcccaaggatt-------tggagctcactctctttcttggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAG
||| || || || | | || || ||| || || | | | || || | | || ||| || || ||||| || ||||||||||||||||| ||||| |||||||| || || || ||||| |||||||| || ||||| ||||| || |||
gtatatatacaaatatattgccacttcattttctttctggctggtgaataacttcccaagtaatctagctgatgctatttgactgaagttttcaaagaacctattcatgcataatagtatcattttggtctggcagGTTCTTCTATGCCTCGAGTGCATGCATTTACCCTGAGTTCAAGCAGCTTGACACAAATGTGAGCTTGAAGGAATCTGATGCCTGGCCTGCTGAG
upper sequence: EFJ36458 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA03G40720.1 (Glycine max), 3'ss of exon 2
--------------------------------gtagcctgtggtgtttctaagttgttcttcccaaggatttggagctcactctctttcttgg-------cttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAG
|| | | | | | || || | | || | | ||| |||| || || ||||||||||| || ||||| || || || || || || |||||| ||||||| || ||||||||||||||||| ||||| ||||| || |||
gtcattcattttgaacaaacatgtgttattatgtcactttcaattgcatgatatagtctttatgtcgccgtcatagtgatccttgttttttggtttattttttttagGTTTTTTTATGCCTCTAGTGCTTGTATCTATCCTGAATTCAAGCAGTTGGAGACAAATGTGAGTTTGAAGGAGTCTGATGCCTGGCCTGCTGAG
upper sequence: EFJ36458 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA10G30400.1 (Glycine max), 3'ss of exon 1
-----------------------------------------gtagcctgtggtgtttctaagttgttcttcccaaggatttggagctcactctctttcttgg--------cttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAG
| | | || | | | | || || || | | | | || |||||| ||||||||||| || ||||| || || ||||| || ||||| ||| |||| ||||| ||||| ||||||||||| ||||||||||| || |||
gttagccatcatgcacatcatttcaattatttgtttttggaccaaacatttatgatgcggtggctgttttgattagatgatgatgtgttttatgcgttctgaaaaatatttttccagGTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGAAACTAATGTGAGCTTGAAGGAGTCCGATGCATGGCCAGCTGAG
upper sequence: EFJ36458 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: AT5G28840.1 (Arabidopsis thaliana), 3'ss of exon 2
--------------gtagcctgtggtgtttctaagtt---gttcttcccaaggatttgga--gctcactctctttcttggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTA---ACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAG
|| || ||| || | || ||| | || | || | | | | ||| || |||| || || |||||||| || ||||| || || || || |||||||||||| ||||||||| | ||||| ||||||||||||||||| ||||| ||||||
gttagttagattttgttttcttcggttttcgcagtttacggtttcttaaaacaagttaaaaagattggattttttgtttgcttt-agGTTCTTTTATGCTTCGAGTGCTTGTATCTATCCAGAGTTTAAGCAGTTGGAGACTACTAATGTGAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAG
upper sequence: EFJ36458 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: Vv14s0030g02180.t01 (Vitis vinifera), 3'ss of exon 2
----------------------------------------------------------------------------------------------gtagcctgtggt-gtttctaagttgttct--tcccaaggatttg--gagctcactctctttcttggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAG
| | | | | | | || |||| ||| || ||| | || | || | | ||| || || ||||| || ||||| ||||| ||||| || ||||||||| |||| ||||| ||||| ||||||||||| ||||||||||| ||||||
gtttgttgtcttcaatttgttctatcctggctttgactaagttctccatttgatatgaaaattggtttcatgtactcagcatttatctgtctaggagacgtaaatttactaatgaatttttctggtcctgagaattctctaatatctgattattccacattgtgcagGTTCTTCTATGCCTCTAGTGCTTGCATCTACCCTGAATTTAAGCAGTTGGAAACTAATGTGAGCTTGAAGGAGTCTGATGCATGGCCTGCAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttctaagttgttcttcccaaggatttggagctcactctctttcttggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAG
agctcac putative branch site (score: 3)
ctcactctctttcttg CT-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagcctgtggtgtttctaagttgttcttcccaaggatttggagctcactctctttcttggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG